Thank you for your response. I got script which calculates full sequence length in fasta file format. But I want add script which will calculate intron length, which is "intron length = full length - exon length". Exon length = Transcription length.

 
#!/usr/bin/perl

use strict;
use warnings;

my $fastaName = "example2.fasta";

open FASTA, $fastaName
  or die "cannot open $fastaName\n";

my $sequence = "";
my $sequencelength;

while ( my $line = <FASTA> ) {
    chomp($line);
    if ( substr( $line, 0, 1 ) eq ">" ) {
        if ( length($sequence) > 1 ) {

            #Calculate sequence lenght
            $sequencelength = length($sequence);

            print "Sequence length: $sequencelength";
            print "\n";
            
            $sequence = "";
        }
        print "$line\n";
    } else {
        $sequence .= $line;
    }
}

#Calculate sequence lenght for last sequence
$sequencelength = length($sequence);


#Print sequence lenght
print "Sequence length: $sequencelength";
print "\n";

[download]

In reply to Re^2: intron length by MBobur
in thread intron length by MBobur

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.